SMED30024968

Overview
NameSMED30024968
Smed IDSMED30024968
Length (bp)506
Neoblast Clusters

Zeng et. al., 2018



 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30024968

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30024968 dd_Smed_v4_13734_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30024968 dd_Smed_v4_13734_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30024968 dd_Smed_v4_13734_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30024968 dd_Smed_v4_13734_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30024968 dd_Smed_v4_13734_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30024968 dd_Smed_v4_13734_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30024968 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001825:67267..67766 -2217
Homology
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BLAST of SMED30024968 vs. Planmine SMEST
Match: SMESG000021486.1 (SMESG000021486.1)

HSP 1 Score: 97.4413 bits (241), Expect = 7.801e-24
Identity = 60/140 (42.86%), Postives = 84/140 (60.00%), Query Frame = 1 
Query:    4 INETKAETLETELNKAKRFLYFVVRDKQMYLSKRKYSYRMPLHSRKICTPIMAGYITDILKNLFAYIXXXXXXEQRQDTLDSLTVEHVIVSEENISKEPSYSIVDDESLETLDNDHETFKRNLEVDIDGIQQNPIETNND 423
            IN  K+E+ +  + KAKRFL+FV+RDK+ +L   KYSYR+PLH RKICT  M  +I  I+++L   +   +++EQ  D  DS+T+ +   S E      S SIVD   +ET   +H   KR LEVDID ++     TN D
Sbjct: 4526 INAIKSESDDETIAKAKRFLFFVIRDKKKFLLGSKYSYRIPLHCRKICTTNMTTHIFSIIQSLLLTL-TVSDSEQIADRSDSITLVNTTQSVEINPGTQSGSIVDISVVETGSTEHARVKRRLEVDIDEVESIIHTTNRD 4664

HSP 2 Score: 88.1965 bits (217), Expect = 1.253e-20
Identity = 53/124 (42.74%), Postives = 75/124 (60.48%), Query Frame = 1 
Query:    4 INETKAETLETELNKAKRFLYFVVRDKQMYLSKRKYSYRMPLHSRKICTPIMAGYITDILKNLFAYIXXXXXXEQRQDTLDSLTVEHVIVSEENISKEPSYSIVDDESLETLDNDHETFKRNLE 375
            IN  K+E+ +  + KAKRFL+FV+RDK+ +L   KYSYR+PLH RKICT  M  +I  I+++L   +   +++EQ  D  DS+T+ +   S E      S SIVD   +ET   +H   KR LE
Sbjct: 2206 INAIKSESDDETIAKAKRFLFFVIRDKKKFLLGSKYSYRIPLHCRKICTTNMTTHIFSIIQSLLLTL-TVSDSEQIADRSDSITLVNTTQSVEINPGTQSGSIVDISVVETGSTEHARVKRRLE 2328
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BLAST of SMED30024968 vs. Planmine SMEST
Match: SMESG000021486.1 (SMESG000021486.1)

HSP 1 Score: 97.4413 bits (241), Expect = 8.348e-24
Identity = 62/158 (39.24%), Postives = 95/158 (60.13%), Query Frame = 1 
Query:    4 INETKAETLETELNKAKRFLYFVVRDKQMYLSKRKYSYRMPLHSRKICTPIMAGYITDILKNLFAYIXXXXXXEQRQDTLDSLTVEHVIVSEENISKEPSYSIVDDESLETLDNDHETFKRNLEVDIDGIQQNPIETNNDHQEDQNTRPFRKTRKTGA 477
            IN  K+E+ +  + KAKRFL+FV+RDK+ +L   KYSYR+PLH RKICT  M  +I  I+++L   +   +++EQ  D  DS+T+ +   S E      S SIVD   +ET   +H   KR LEVDID + ++ I T +  Q++  ++    +++T A
Sbjct: 2206 INAIKSESDDETIAKAKRFLFFVIRDKKKFLLGSKYSYRIPLHCRKICTTNMTTHIFSIIQSLLLTL-TVSDSEQIADRSDSITLVNTTQSVEINPGTQSGSIVDISVVETGSTEHARVKRRLEVDIDEV-ESIIHTTSGTQQNHISKSALISKETDA 2361

HSP 2 Score: 96.2857 bits (238), Expect = 2.235e-23
Identity = 57/132 (43.18%), Postives = 81/132 (61.36%), Query Frame = 1 
Query:    4 INETKAETLETELNKAKRFLYFVVRDKQMYLSKRKYSYRMPLHSRKICTPIMAGYITDILKNLFAYIXXXXXXEQRQDTLDSLTVEHVIVSEENISKEPSYSIVDDESLETLDNDHETFKRNLEVDIDGIQQ 399
            IN  K+E+ +  + KAKRFL+FV+RDK+ +L   KYSYR+PLH RKICT  M  +I  I+++L   +   +++EQ  D  DS+T+ +   S E      S SIVD   +ET   +H   KR LEVDID ++ 
Sbjct: 4555 INAIKSESDDETIAKAKRFLFFVIRDKKKFLLGSKYSYRIPLHCRKICTTNMTTHIFSIIQSLLLTL-TVSDSEQIADRSDSITLVNTTQSVEINPGTQSGSIVDISVVETGSTEHARVKRRLEVDIDEVES 4685
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BLAST of SMED30024968 vs. Planmine SMEST
Match: SMESG000052959.1 (SMESG000052959.1)

HSP 1 Score: 78.1814 bits (191), Expect = 3.541e-17
Identity = 50/119 (42.02%), Postives = 73/119 (61.34%), Query Frame = 1 
Query:  130 HSRKICTPIMAGYITDILKNLFAYIXXXXXXEQRQDTLDSLTVEHVIVSEENISKEPSYSIVDDESLETLDNDHETFKRNLEVDIDGIQQNPIETNNDHQEDQNTRPFRKTRKTGAKNK 486
              RKICT  +A +IT++LKNLF ++N   + ++R+   DS  VE+VIV  E ISK    S+V+ + L T DN +E   +  +VDIDGIQ   + + N    +Q+T+P R TR+T  K K
Sbjct:  384 QCRKICTSNIAWHITEMLKNLFTFLNKITS-DKRKGKSDSSAVENVIVLGETISKNSFQSLVESDMLNTPDNTNENVNQMPQVDIDGIQPTSVASIN----EQHTKPQRTTRQTVVKTK 497

HSP 2 Score: 56.6102 bits (135), Expect = 1.008e-9
Identity = 29/55 (52.73%), Postives = 34/55 (61.82%), Query Frame = 1 
Query:  340 DNDHETFKRNLEVDIDGIQQNPIETNNDHQEDQNTRPFRKTRKTGAKNK*RCVPA 504
            +ND E   R LEVDID IQQ  I T+ND  E Q TRP++K  K   +   RCVPA
Sbjct:  225 NNDSEILNRKLEVDIDEIQQIAIATSNDQHEYQQTRPYKKVGKQVPRLNGRCVPA 279
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BLAST of SMED30024968 vs. Planmine SMEST
Match: SMESG000059599.1 (SMESG000059599.1)

HSP 1 Score: 60.077 bits (144), Expect = 5.495e-11
Identity = 28/69 (40.58%), Postives = 43/69 (62.32%), Query Frame = 1 
Query:   46 KAKRFLYFVVRDKQMYLSKRKYSYRMPLHSRKICTPIMAGYITDILKNLFAYIXXXXXXEQRQDTLDSL 252
            KAK  +YF +RDK+ ++S +K SYR+P   RKICT  M+G+I  I+ +L  +I   ++  Q     +SL
Sbjct:   69 KAKCLIYFAIRDKEKFISSKKQSYRIPQTCRKICTSKMSGFIFQIIDSLVLFIEEKSDVNQVAKPTNSL 137
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BLAST of SMED30024968 vs. Planmine SMEST
Match: SMESG000013454.1 (SMESG000013454.1)

HSP 1 Score: 59.6918 bits (143), Expect = 8.474e-11
Identity = 24/50 (48.00%), Postives = 39/50 (78.00%), Query Frame = 1 
Query:   37 ELNKAKRFLYFVVRDKQMYLSKRKYSYRMPLHSRKICTPIMAGYITDILK 186
            +L KAKR LYF++RDK+ +L+K  ++YR+P + RKICT  M+ +IT +++
Sbjct:  343 DLVKAKRMLYFIIRDKKRFLNKDNFNYRIPFNCRKICTLKMSDFITKLIQ 392
The following BLAST results are available for this feature:
BLAST of SMED30024968 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024968 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024968 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024968 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024968 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024968 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024968 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024968 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024968 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024968 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024968 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024968 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024968 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30024968 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000021486.17.801e-2442.86SMESG000021486.1[more]
SMESG000021486.18.348e-2439.24SMESG000021486.1[more]
SMESG000052959.13.541e-1742.02SMESG000052959.1[more]
SMESG000059599.15.495e-1140.58SMESG000059599.1[more]
SMESG000013454.18.474e-1148.00SMESG000013454.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024968 ID=SMED30024968|Name=SMED30024968|organism=Schmidtea mediterranea sexual|type=transcript|length=506bp
ATTATTAATGAGACTAAAGCTGAAACACTTGAAACAGAGTTAAATAAAGC
TAAGCGATTTTTATACTTTGTTGTTAGAGACAAACAAATGTATTTATCTA
AAAGAAAATACTCATACCGCATGCCTTTACACAGCAGAAAGATTTGCACA
CCTATCATGGCTGGATACATCACAGACATACTTAAAAATCTCTTTGCATA
TATTAATAATAATAACAACAACGAACAAAGGCAAGACACGCTTGACTCTC
TCACTGTAGAACATGTCATTGTATCTGAAGAGAATATCTCAAAAGAACCA
TCATATTCTATTGTCGACGATGAGTCACTTGAAACTTTAGATAACGACCA
TGAGACTTTTAAACGAAACCTAGAAGTTGACATTGATGGAATTCAACAAA
ACCCTATAGAGACTAATAATGATCATCAAGAAGACCAGAATACAAGGCCA
TTTAGAAAAACTAGAAAAACAGGTGCCAAGAATAAATGAAGGTGCGTGCC
TGCATC
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protein sequence of SMED30024968-orf-1

>SMED30024968-orf-1 ID=SMED30024968-orf-1|Name=SMED30024968-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=163bp
IINETKAETLETELNKAKRFLYFVVRDKQMYLSKRKYSYRMPLHSRKICT
PIMAGYITDILKNLFAYINNNNNNEQRQDTLDSLTVEHVIVSEENISKEP
SYSIVDDESLETLDNDHETFKRNLEVDIDGIQQNPIETNNDHQEDQNTRP
FRKTRKTGAKNK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 66..85